Locus 1029

Sequence ID X_DroMel_CAF1
Location 3,005,805 – 3,006,150
Length 345
Max. P 0.986258
window1658 window1659 window1660 window1661

overview

Window 8

Location 3,005,805 – 3,005,918
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 83.93
Mean single sequence MFE -27.10
Consensus MFE -15.56
Energy contribution -15.06
Covariance contribution -0.50
Combinations/Pair 1.16
Mean z-score -2.39
Structure conservation index 0.57
SVM decision value 0.32
SVM RNA-class probability 0.687680
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3005805 113 + 22224390
AAGCAAGCGAUCGCAAAGAGCCACAUAAAAUAAGCUAAGGUUU--UUCGAACGCAGA-----GAGGAAAGCCAACAACGAGAGCGAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGC
......((((((.((....(((((((.......(((..(((((--(((.........-----..))))))))..(.....))))(((.....)))......)))))))...)))))).)) ( -24.40)
>DroSec_CAF1 382649 102 + 1
AAG----CGAUCGU-AAGAGCCACAUAAA---AGCUAAGGUUU--CUCGGACGCAGA-----GAGGAAAGCCAA---CCAGAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGC
..(----(((((..-....(((((((...---.(((..(((((--(((.......))-----))((....))))---))..)))..(((........))).))))))).....)))).)) ( -25.50)
>DroEre_CAF1 414413 103 + 1
AAG----CGAUCG--AGGAGCCACAUAAA---AGCUAAGGUUUUUUUUGGACGCAGA-----GAGAAAAGCCAA---GCAGAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGC
..(----(((((.--(...(((((((...---.(((..((((((((((.........-----)))))))))).)---)).......(((........))).)))))))...).)))).)) ( -26.20)
>DroYak_CAF1 395722 107 + 1
AAG----CGAUCGC-AAGAGCCGCAUAAA---AGCUAAGGUUU--UGUGGACACAGACUUUUGCGCUCUGCCAA---CCAGAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGC
..(----(((((.(-(...(((((((...---.((.(((((((--.((....))))))))).))((((((....---.)))))).................)))))))...)))))).)) ( -32.30)
>consensus
AAG____CGAUCGC_AAGAGCCACAUAAA___AGCUAAGGUUU__UUCGGACGCAGA_____GAGGAAAGCCAA___CCAGAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGC
........((((.......(((((((.......(((..(((((..(((..............)))..))))).........)))..(((........))).))))))).....))))... (-15.56 = -15.06 +  -0.50) 

alignment

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secondary structure

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Window 9

Location 3,005,878 – 3,005,995
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.36
Mean single sequence MFE -29.50
Consensus MFE -24.44
Energy contribution -24.25
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.47
Structure conservation index 0.83
SVM decision value 1.54
SVM RNA-class probability 0.962162
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3005878 117 + 22224390
GAGCGAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGCA-UGGAUCAACCGUAAACGAUCCGAGGAUCAGUUGGCCUGGGCCACAAGACCGAA--AAAAAAAAAACAGCUCUAAUAGC
(((((((.....))).......((((((....((.((((((-(((.....))))....((((....)))).)))))))...))))))........--............))))....... ( -31.10)
>DroSec_CAF1 382711 112 + 1
GAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGCA-UGGAUCAACCGUAAACGAUCCGAGGAUCAGUUGGCCUGGGCCACAAGACCGAA--AA-----AAUCAGCUCUAAUAGC
((((..(((........)))..((((((....((.((((((-(((.....))))....((((....)))).)))))))...))))))........--..-----.....))))....... ( -30.20)
>DroEre_CAF1 414476 108 + 1
GAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGCA-UGGAUCAACCGUAAACGAUCCGAGGAUCAGUU------GGCCACAAGACCGAACAGA-----AAUCAGCUCUAAUAGC
((((..(((........)))..((((((.(((.((((....-((((((..........))))))..)))).)))------.))))))............-----.....))))....... ( -26.90)
>DroYak_CAF1 395789 112 + 1
GAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGCAACGGAUCAGUCGUAAACGAUCCGAGGAUCAGUUGUUGU-GGCCACAAGACCGAA--AA-----AAUCAGCUCUAAUAGC
((((..(((........)))....((((...(((..(((((((.((((.((((....)))).....)))).))))))).-..)))....))))..--..-----.....))))....... ( -29.80)
>consensus
GAGCAAUUCCAAAUCAAGAAAAUGUGGUAAAUGGAUCAGCA_UGGAUCAACCGUAAACGAUCCGAGGAUCAGUUGGCCU_GGCCACAAGACCGAA__AA_____AAUCAGCUCUAAUAGC
((((..(((........)))..((((((.(((.((((.....((((((..........))))))..)))).))).......))))))......................))))....... (-24.44 = -24.25 +  -0.19) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,005,918 – 3,006,035
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.36
Mean single sequence MFE -34.95
Consensus MFE -30.88
Energy contribution -31.12
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.88
SVM decision value 2.04
SVM RNA-class probability 0.986258
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3005918 117 - 22224390
UUGGCGAUAAGAUCGCUUUGAACUUUUGUCUUGAGCUUGAGCUAUUAGAGCUGUUUUUUUUUU--UUCGGUCUUGUGGCCCAGGCCAACUGAUCCUCGGAUCGUUUACGGUUGAUCCA-U
..(((.((((((((((((...((....))...))))...((((.....))))...........--...)))))))).)))(((.....)))......((((((........)))))).-. ( -34.50)
>DroSec_CAF1 382751 112 - 1
UUGGCGAUAAGAUCGCUUUGAACUUUUGUCUUGAGCUUGAGCUAUUAGAGCUGAUU-----UU--UUCGGUCUUGUGGCCCAGGCCAACUGAUCCUCGGAUCGUUUACGGUUGAUCCA-U
..........(((((((.(((((.......(((.(((((.(((((.(((.((((..-----..--.))))))).))))).))))))))..((((....))))))))).)).)))))..-. ( -35.60)
>DroEre_CAF1 414516 108 - 1
UUGGCGAUAAGAUCGCUUUGAACUUUUGUCUUCAGCUUGAGCUAUUAGAGCUGAUU-----UCUGUUCGGUCUUGUGGCC------AACUGAUCCUCGGAUCGUUUACGGUUGAUCCA-U
(((((.((((((((.....((((....(...(((((((.........)))))))..-----.).)))))))))))).)))------)).........((((((........)))))).-. ( -35.60)
>DroYak_CAF1 395829 112 - 1
UUGGCGAUAAGAUCGCUUUGAACUUUUGUCUUGAGCUUGAGCUAUUAGAGCUGAUU-----UU--UUCGGUCUUGUGGCC-ACAACAACUGAUCCUCGGAUCGUUUACGACUGAUCCGUU
.((((.(((((((((((((((.(((..((.....))..)))...))))))).((..-----..--.)))))))))).)))-)..............(((((((........))))))).. ( -34.10)
>consensus
UUGGCGAUAAGAUCGCUUUGAACUUUUGUCUUGAGCUUGAGCUAUUAGAGCUGAUU_____UU__UUCGGUCUUGUGGCC_AGGCCAACUGAUCCUCGGAUCGUUUACGGUUGAUCCA_U
..(((.((((((((((((...((....))...))))...((((.....))))................)))))))).))).................((((((........))))))... (-30.88 = -31.12 +   0.25) 

alignment

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secondary structure

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dotplot

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Window 1

Location 3,006,035 – 3,006,150
Length 115
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.58
Mean single sequence MFE -20.33
Consensus MFE -15.98
Energy contribution -15.97
Covariance contribution -0.00
Combinations/Pair 1.05
Mean z-score -1.44
Structure conservation index 0.79
SVM decision value 0.01
SVM RNA-class probability 0.538416
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3006035 115 + 22224390
AUCA-AAAAGAAAAACAAACCAAAAAAAUGGCUUACAGAAAGAGGGGCCAGCACAUA----UACACAUGGCAUGGCCAUUGGCUUGAUCGUGCCUUUGAUGAUCAUCGCAAAACCAAAAC
....-..............(((......)))............(((((((((.(((.----.....))))).)))))....((.(((((((.......)))))))..))....))..... ( -24.90)
>DroSec_CAF1 382863 104 + 1
AUCA-AA-----AAACAAACCAAA-AAAUGGCUUACAGAAAGAGGGGCCAGCACAUA----UACACAU-----GGCCAUUGGCUUGAUCGUGCCUUUGAUGAUCAUCGCAAAACCAAAAC
....-..-----.......(((..-...)))............(((((((.......----......)-----))))....((.(((((((.......)))))))..))....))..... ( -19.72)
>DroEre_CAF1 414624 105 + 1
AUCACAA-----AAACAAACCGAA-AAAUGGCUUAAAGAAAGAGAGGGCAGCACAUA----UACACAU-----GGCCAUUGGCUUGAUCGUGCCUUUGAUGAUCAUCGCAAAACCAAAAA
.......-----............-.(((((((.............(......)...----.......-----))))))).((.(((((((.......)))))))..))........... ( -14.80)
>DroYak_CAF1 395941 107 + 1
AUCA-AA-----AAACAAACCAAA-AAAUGGCUUCAAGAAAGAGAGGCCAGCACAUACACAUACACAU-----GGCCAUUGGCUUGAUCGUGCCUUUGAUGAUCAUCGCAAAACCAAAA-
....-..-----............-...(((((((........)))))))((................-----((((...))))(((((((.......)))))))..))..........- ( -21.90)
>consensus
AUCA_AA_____AAACAAACCAAA_AAAUGGCUUAAAGAAAGAGAGGCCAGCACAUA____UACACAU_____GGCCAUUGGCUUGAUCGUGCCUUUGAUGAUCAUCGCAAAACCAAAAC
............................((((((..........))))))((.....................((((...))))(((((((.......)))))))..))........... (-15.98 = -15.97 +  -0.00) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:41 2006